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Modules in NISO STS
This section names and describes all of the modules of the NISO STS that exist in
the base Interchange and Extended Tag Sets in the DTD forms. An organization may choose
to add additional modules or not call in some of those listed.
The Four NISO STS Tag Sets
Each of the NISO STS Tag Sets will have its own DTD module. The individual DTD modules
call in all of the other modules needed and then declare the top-level <standard> element.
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NISO-STS-interchange-1-mathml2.dtd
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The base NISO STS Interchange Tag Set, using MathML 2.0, for organizations already
using MathML 2.0. This Tag Set is intended not recommended for new users or users
who are not already tagging math.
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NISO-STS-interchange-1-mathml3.dtd
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The base NISO STS Interchange Tag Set, using MathML 3.0. Using MathML 3.0 is Best
Practice, preferred over MathML 2.0.
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NISO-STS-extended-1-mathml2.dtd
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The Extended version of the NISO STS Tag Set, which includes both XHTML and CALS tables
and uses MathML 2.0. This Tag Set is intended for organizations already using MathML
2.0 and is not recommended for new users or users who are not already tagging math.
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NISO-STS-extended-1-mathml3.dtd
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The Extended version of the NISO STS Tag Set, which includes both XHTML and CALS tables
and uses MathML 3.0. Using MathML 3.0 is Best Practice, preferred over MathML 2.0.
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NISO-STS-specific Customizations
The NISO STS customization modules are used in each of the NISO STS DTDs to declare
NISO-STS-specific elements and provide overrides for the JATS Publishing, JATS Suite,
and BITS modules. The filename for each modules will include a version number and
a suffix (.ent), so, for example, the module “NISO-STS-modules” will in this version of NISO STS, take a filename of “NISO-STS-modules1.ent”.
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NISO-STS-modules
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Module to Name NISO STS Suite-specific Module — Declares all the external modules
that are specific to NISO STS (except this module itself, so this module must be both
declared and called from inside a DTD). A Tag Set selects from these modules by referencing
the module names through external parameter entities. All modules are declared (named)
in this Module of Modules, but referenced (called in, if wanted) inside a DTD. To
include a set of elements (such as all the non-TBX terms and definitions elements),
a DTD references the external parameter entity of the module that contains these declarations.
Call-in Sequence: The NISO STS Module to Name NISO STS Suite-specific Modules is the first of the naming
modules. Each NISO STS Tag Set also contains the Journal Publishing Tag-Set-specific
Module of Modules and the JATS base Module to Name the Modules (along with the MathML
3 modules, if used). These modules need to be among the first four external modules
called by a NISO STS Tag Set. Customization modules for classes, mixes, and models
will typically be called following the cluster of Modules to Name the Modules.
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NISO-STS-classes
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NISO STS DTD Customize Classes Module — Sets up the parameter entities for class overrides.
These
parameter entities will over-ride selected class definitions in the JATS
Journal Publishing DTD class module, the JATS base suite default class module, and
selected BITS modules.
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NISO-STS-classes-extended
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NISO STS Extended DTD Customize Classes Module
— Sets up the parameter entities for element
class overrides that override the NISO STS
ordinary classes when OASIS tables are
used in a Tag Set.
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NISO-STS-mixes
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NISO STS DTD Customize Mixes Module — Sets up the parameter entities for mix overrides.
These parameter entities will over-ride
selected mix definitions in the JATS
Journal Publishing DTD mix module, the JATS base suite mix module, and selected BITS
modules.
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NISO-STS-models
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NISO STS DTD Customize Content Models and Attributes Module — Sets up the parameter
entities for complete content
models, element-groups within content models, attribute lists, and attribute value
overrides. These parameter entities will over-ride selected
content models and attribute lists in the JATS Publishing
DTD, the JATS base suite, and selected BITS modules.
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NISO STS Element Definition Modules
These modules, which define the NISO-STS-specific elements and attributes, are the
base of NISO STS and are shared by all NISO STS Tag Sets:
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NISO-STS-adoption
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NISO STS Top-level Adoption Wrapper Module — Element declarations for the top-level
<adoption> element in the NISO STS Interchange Tag Sets.
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NISO-STS-adoption-extended
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NISO STS CALS Top-level Adoption Wrapper Module — Element declarations for the NISO
STS top-level <adoption> element in the Extended Tag Sets (which include CALS tables).
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NISO-STS-standards-components
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NISO-STS-notes-exmp
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NISO STS Notes and Examples Elements Module — Element declarations for both normative
and non-normative notes and
examples.
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NISO-STS-terms-n-def
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Non-TBX Terms and Definitions Section Modules — Declares the elements for a less complex,
reading-order model for
terms and definitions, which may be used
instead of or in addition to the TBX term models.
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NISO-STS-common-metadata
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NISO STS Common Metadata Elements Module — Declares the metadata elements shared by
all of
the metadata components elements (<std-meta>, <iso-meta>, etc.) and their
contents.
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NISO-STS-std-metadata
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NISO STS Standards Metadata Elements Module — Declares the <std-meta> element.
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NISO-STS-iso-metadata
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NISO STS ISO Metadata Elements Module — Declares the <iso-meta> element.
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NISO-STS-nat-metadata
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NISO STS ISO-related National Metadata Elements Module — Declares the <nat-meta> element.
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NISO-STS-reg-metadata
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NISO STS ISO-related Regional Metadata Elements Module — Declares the <reg-meta> element and its unique contents.
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NISO-STS-tbx-setup
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NISO STS TBX Setup Module — Declares the elements and attributes for describing terms
and definitions in a namespace-qualified, TBX (TermBase eXchange) compatible vocabulary
derived from ISO 30042.
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NISO-STS-tbx-namespace
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NISO STS TBX Namespace Module — Provides the namespace structure for using the namespace-qualified
version of the TBX DTD. The NISO STS TBX elements define the TBX (TermBase eXchange)
vocabulary, and are based on ISO 30042:2008(E)
Annex A, modified to make all the STS TBX elements
be namespace-qualified.
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Modules Shared with JATS Publishing DTD
The JATS Publishing DTD modules are an integral part of NISO STS, as they were of
ISO STS. NISO STS customization modules override portions of the JATS Publishing customization
modules, which in term override JATS base-Suite modules. The customization modules
of the JATS Journal Publishing Tag Set (JATS-journalpubcustom-classes1-3.ent, JATS-journalpubcustom-mixes1-3.ent, JATS-journalpubcustom-models1-3.ent, and JATS-journalpubcustom-modules1-3.ent, and, for the extended NISO Tag Sets the modules JATS-journalpub-oasis-custom-classes1-3.ent and JATS-journalpub-oasis-custom-modules1-3.ent) are used directly inside NISO STS DTDs.
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JATS-journalpubcustom-modules
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Module to Name Journal Publishing Tag-Set-specific Modules Module — Declares all the
external modules that are specific to the JATS Journal Publishing Tag Set (except
itself, so this module must be both named and called inside a DTD). A Tag Set selects
from these modules by referencing the module names through external parameter entities.
The entities are declared in this module, but referenced (or not) inside a NISO STS
DTD. To include a set of elements (such as all the lists or all the MathML elements),
a DTD references the external parameter entity of the module that contains these declarations.
In NISO STS, this Module of Modules joins those for NISO STS and the JATS base-Suite.
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JATS-modules
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JATS Base-Suite Module to Name the Modules Module — Declares all the external modules
that are part of the modular JATS DTD Suite (except itself, which must be both named
and called inside a DTD).
In NISO STS, this Module of Modules joins those for NISO STS and the JATS Publishing
DTD.
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JATS-journalpubcustom-classes
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JATS Journal Publishing Tag Set Class Customizations Module — Declares the parameter
entities that will be used to override default classes prescribed by the JATS-default-classes module.
Implementor’s Note: This module must be called after the various Module to name the Modules, but before
any other JATS-specific modules, including specifically the JATS-default-classes module (which this module overrides) and the JATS-journalpubcustom-mixes module (which builds on components defined in this module).
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JATS-default-classes
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JATS Default Element Classes Module — Declares the parameter entities that name the
element members of each class that will be used to establish the content models.
Implementor’s Note: This module must be called before any of the mixes modules, as well before the Journal
Publishing Customize Models Module (JATS-journalpubcustom-models, which builds on those modules).
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JATS-journalpubcustom-mixes
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Journal Publishing Tag Set Mix Customizations Module — Declares the parameter entities
that will be used to override default mixes (groupings made of “classes”) prescribed
by the JATS-default-mixes module.
Implementor’s Note: This module must be called after all the JATS classes modules, but before the JATS-default-mixes module (which this module overrides) and the JATS-journalpubcustom-models module (which builds on this module).
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JATS-default-mixes
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JATS Base-Suite Default Element Mixes Module — Declares the parameter entities that
name mixes (groupings made of “classes”) that will be used to establish the content
models.
Implementor’s Note: This module must be called before the Journal Publishing Customize Models Module
(JATS-journalpubcustom-models) or any element-defining modules of the Suite.
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JATS-journalpubcustom-models
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Journal Publishing Tag Set Models/Attributes Customizations Module — Declares the
parameter entities that will be used to override content model parameter entities
set elsewhere in the Suite. Also defines customizable attribute Declared Values and
attribute lists for the tag set being defined.
Implementor’s Note: This module must be called after all the class and mixes modules, but before any
of the element-defining modules of the Suite.
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Modules Shared with BITS
The following modules are used as part of NISO STS, unchanged from BITS. Their content
may be overridden by NISO-STS-specific customizations.
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BITS-index
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BITS Structural Index Elements Module — Element declarations for the BITS structural
index model (<index>).
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BITS-embedded-index
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BITS Embedded Index Elements Module — Element declarations for the index elements
that are embedded in the document
narrative for the autogeneration of indexes.
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BITS-toc
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BITS Structural Table of Contents Module — Element declarations for the BITS structural
Table of Contents model.
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BITS-toc-index-nav
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BITS Structural Navigation Module — Element declarations for the BITS navigation
and pointing mechanism for structural
Indexes and Tables of Contents.
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BITS-xinclude
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BITS Xinclude Module — Sets up the namespace and elements for using
<xi:include> to manage standards and adoptions as components rather than as a whole.
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Modules Shared with JATS Suite
The following modules are used as part of NISO STS, unchanged from the JATS common
modules. Their content may be overridden by NISO-STS-specific customizations.
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JATS-ali-namespace
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ALI Namespace Module — Namespace setup for the NISO Access License and Indicators
elements (prefix “ali:”). The ALI elements are defined in the JATS Common
module (described hereafter).
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JATS-common-atts
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JATS Common (Shared) Attributes Module — Declares the attributes intended to be used
on
ALL elements defined in the NISO JATS. The list of all elements includes the table elements
for both the
XHTML-inspired and OASIS-inspired table
models. The list of all elements does not include <mml:math> and its contents, whose namespaces NISO STS does not control.
This module must be called after all module-of-modules
modules and any namespacing modules, but
before all customization (over-ride) modules.
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JATS-common
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JATS Common (Shared) Elements Module — Declarations for elements, attributes, entities,
and notations that are shared by
more than one class module or tag set.
Implementor’s Note: This module must be called before any of the NISO-STS-specific element grouping modules
in the NISO STS Suite, but after the NISO STS models module and the JATS Publishing
models module.
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JATS Element and Attribute Definition Modules
The modules that declare the structural and elements and attributes that make up the
JATS base-Suite are defined
by the following modules. These models and attribute lists may be overridden by the
customization modules of NISO STS or of the JATS Publishing DTD.
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JATS-articlemeta
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JATS Journal Article Metadata Elements Module — Declares the metadata elements (issue
elements and article header elements) originally used to describe a journal article,
but now included among the metadata elements for standards documents.
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JATS-backmatter
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JATS Back Matter Elements Module — Declares elements that are not part of the main
textual flow of a work, but are considered to be ancillary material that follows the
main document, such as appendices, glossaries, and bibliographic reference lists.
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JATS-display
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JATS Display Class Elements Module — Declares the display-related elements, such as
figures, graphics, chemical expressions and structures, tables, etc.
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JATS-format
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JATS Format Class Elements Module — Declares elements concerned with rendition of
output, for example, printing on a page or displaying on a screen. For example, this
module declares elements in the Appearance Class, the Break Class, and the Emphasis
(typographic highlighting) Class.
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JATS-funding
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JATS Funding Elements Module — Declares elements that model open access, grant, sponsorship,
or other funding information, for example, the grant number (<award-id>).
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JATS-link
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JATS-list
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JATS List Class Elements Module — Declares the elements in the List Class; these include
all lists except normative and non-normative lists of bibliographic references (citations).
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JATS-math
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JATS Math Class Elements Module — Declares the elements in the math classes such as
display equations.
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JATS-nlmcitation
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Former JATS NLM Citation Module — Adds the model for the NLM structured bibliographic
citation element (<nlm-citation>). This element is now obsolete, has been deprecated in JATS, and should be replaced
by either the <mixed-citation> or the <element-citation> element.
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JATS-para
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JATS Paragraph-Like Elements Module — Declares structural, non-display elements that
may appear in the same places as a paragraph (such as <statement> or <disp-quote>). These elements are named in the various paragraph class parameter entities.
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JATS-phrase
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JATS Subject Phrase Class Elements Module — Declares the Phrase Class elements, that
is, names inline elements such as <named-content> and <styled-content>.
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JATS-references
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JATS Bibliographic Reference (Citation) Class Elements Module — Declares the bibliographic
reference component elements (such as <source> and <person-group>).
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JATS-related-object
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JATS Related Object Elements Module — Defines the container element <related-object>, which is used as a container for text links to a related object, possibly accompanied
by a very brief description of the object.
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JATS-section
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JATS Section Class Elements Module — Declares the elements of the Section Class, that
is, declares all section-level elements in JATS.
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MathML Modules
The modules that define or customize the elements and attributes of MathML 2.0 and
MathML 3.0.
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JATS-mathmlsetup
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JATS MathML 2.0 Setup Module — Invokes the MathML 2.0 modules.
Implementor’s Note:: To include the MathML 2.0
elements, a DTD must reference this module. This module sets up all parameter entities
needed to use
the MathML 2.0 Tag Set and references (invokes) the MathML 2.0 Tag Set Module, which,
in turn,
invokes all the other MathML 2.0 modules. MathML Warning: MathML 2.0 and MathML 3.0 may not be used together; a Tag Set must choose one or
the other. Namespace Warning: The MathML setup modules and MathML modules establish the namespaces for MathML and
XLink. Because of XLink, you will need to include the MathML modules, even if you are not using MathML.
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JATS-mathml3-mathmlsetup
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JATS MathML 3.0 Setup Module — Invokes the MathML 3.0 modules.
Implementor’s Note:: To include the MathML 3.0
elements, a DTD must reference this module. This module sets up all parameter entities
needed to use
the MathML 3.0 Tag Set and references (invokes) the MathML 3.0 Tag Set Module, which,
in turn,
invokes all the other MathML 3.0 modules. MathML Warning: MathML 2.0 and MathML 3.0 may not be used
together; a Tag Set must choose one or the other. Namespace Warning: The MathML setup modules and MathML modules establish the namespaces for MathML and
XLink. Because of XLink, you will need to include the MathML modules, even if you are not using MathML.
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JATS-mathml3-modules
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JATS MathML 3.0 Modules Module — Names the modules needed for MathML 3.0.
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mathml2.dtd and mathml3.dtd
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MathML DTDs Modules — Used for either the Mathematical Markup Language (MathML) 2.0
or the MathML 3.0, an XML application for describing mathematical notation and capturing
both its structure and content.
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mathml2-qname.mod and mathml3-qname.mod
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MathML Qualified Names Module — Declares parameter entities to support namespace-qualified
names, namespace
declarations, and name prefixing for MathML, as well as declares the parameter
entities used to provide namespace-qualified names for all MathML element types. Used
for
MathML 2.0 or MathML 3.0, respectively.
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mmlextra
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Extra Entities for MathML Module — Declares MathML entities. The same file is used
for both MathML 2.0 and MathML 3.0 processing.
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mmlalias
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Aliases for MathML Module — The same file is used
for both MathML 2.0 and MathML 3.0 processing.
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XHTML-inspired Table Modules
The modules that define the JATS XHTML-inspired table model are listed below. These
models and attribute lists may be overridden by the customization modules of the NISO
STS or of the JATS Publishing DTDs.
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JATS-XHTMLtablesetup
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NISO JATS XHTML-inspired Table Setup Module — Sets all parameter entities needed by
the NISO JATS XHTML-inspired Table Module, and then invokes the module containing
that model.
To include the NISO JATS XHTML-inspired table model in a tag set, a DTD
must reference this module. This module sets up all parameter entities needed to use
the XHTML-inspired Table Module and references (invokes) the JATS XHTML-inspired Table
Module. (See next item.)
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xhtml-table-1.mod
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NISO JATS XHTML-inspired Table Module — The public XML DTD version of the XHTML-inspired
Table Module. This module is invoked from
the module JATS-XHTMLtablesetup.ent. (See
previous item.) This is the default table model for NISO STS. In the extended Tag
Sets, the OASIS Exchange CALS table model may be used in addition or instead of the
XHTML table model.
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xhtml-inlstyle-1.mod
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OASIS Exchange (CALS) Table Modules
The modules that define the JATS version of the OASIS Exchange (CALS) table model
are listed below. These models and attribute lists may be overridden by the customization
modules of the NISO STS or of the JATS Publishing DTDs. To include the CALS table
model in a Tag Set, these modules must be called out in the DTD.
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JATS-journalpub-oasis-custom-modules
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Journal Publishing DTD OASIS Tables DTD-Specific Modules Module — Declares the DTD-specific
modules necessary to include OASIS Tables.
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JATS-journalpub-oasis-custom-classes
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JATS Journal Publishing DTD with OASIS Tables Customize Classes Module — The class
overrides necessary for CALS tables. These repeat all the class overrides of the regular
Publishing DTD, with the table and alternative
classes modified to use the OASIS XML Exchange (CALS) table elements. There is no
equivalent mix
override module, because CALS processing uses the ordinary Publishing mix overrides.
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JATS-oasis-namespace
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JATS OASIS Table Namespace Module — This modules establishes
the prefix for the OASIS
Exchange (CALS) table model, by default “oasis”
(“<oasis:table>”).
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JATS-oasis-tablesetup
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JATS Namespaced OASIS XML Table Setup Module — Sets all parameter entities
needed by the OASIS XML Exchange (CALS) table model, and then invokes the module
containing that model.
To include the OASIS XML Exchange (CALS) table model, a DTD must reference
this module. This module sets up all parameter entities needed to use the OASIS
table model and references (invokes) the OASIS XML Exchange (CALS) Table Model Module.
This module has been modified to use a hard-coded namespace
prefix of “oasis” for all table elements, to permit both the OASIS
Exchange (CALS) table models and XHTML-inspired table models to be used
in one tag set. There is a separate Tag
Library (https://jats.nlm.nih.gov/options/OASIS/tag-library/19990315/index.html) describing the OASIS elements, attributes, and parameter entities.
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oasis-exchange
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OASIS XML Exchange (CALS) Table Model Module — This is the OASIS XML Exchange (CALS)
table model DTD fragment, modified to use the OASIS namespace and
the “oasis” prefix. This module is invoked from the JATS OASIS XML Exchange
(CALS) setup module (JATS-oasis-tablesetup.ent).
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Character Entities and Notations
The modules that define sets of general entity character entities and the notations
(all optional) are listed below.
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JATS-xmlspecchars
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JATS XML Special Characters Module — Standard ISO XML special character entities used
in this Tag Set.
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JATS-chars
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JATS Custom Special Characters Module — Custom special character entities created
specifically for use in this Tag Set.
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JATS-notat
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JATS Notation Declarations Module — Container module for the Notation Declarations
to be used with this Suite. These notations have been placed in their own module for
easy expansion or replacement. Notations are left over from SGML, were often used
in the early days of JATS, and are far less useful now.
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